Transcriptome assembly v1.0 in development

1) in silico spike-in
2) cut, trim and QC
3) normalize
4) merge paired reads
5) assemble!

Updated README.txt
Update to script to simulate mRNAseq reads for in silico spike-in to validate transcriptome assembly. New script to perform complete in silico transcriptome assembly to validate that the in silico reads will assemble at all.
Debugging transcriptome assembly simulation
Debugging transcriptome simulation script. Ready up to actual assembly stage
Completed simulation of Illumina sequencing through mapping and gene counts. Looks like it's working! Started modifications to files for 'true' assembly
Transcriptome simulation has become a large enough process to warrant it's own repository for development and so as not to confuse with Aphaenogaster transcriptome assembly. Moved to https://github.com/johnstantongeddes/sim-transcriptome
Updating digital normalization prior to velvet-oases assembly on antlab. Added general scripts (some linked from khmer/scripts) to general scripts directory for working with fastq files
Re-organized and modified scripts for transcriptome assembly to perform digital normalization
prior to merging reads and then assembly.

Three workflows

1) trim - assemble (on mason branch merged with master)
2) trim - diginorm - assemble (on transcriptome branch)
3) trim - diginorm - merge overlapping reads - assemble (on transcriptome branch)
Merge branch 'transcriptome'

Conflicts:
	projects/ApTranscriptome/scripts/01-A22-TrimClip-mason.sh
	projects/ApTranscriptome/scripts/01-A22-TrimClip.sh
	projects/ApTranscriptome/scripts/02-A22-TrimClip.sh
	projects/ApTranscriptome/scripts/03-A22-diginorm.sh
	projects/ApTranscriptome/scripts/04-A22-velveth.sh